rcpp_KaKs: rcpp_KaKs

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

rcpp_KaKs

Description

calculates KaKs as implememted in KaKs Calculator 2.0 MSA2dist with Rcpp.

Usage

rcpp_KaKs(cdsstr, sgc = "1", method = "YN", verbose = FALSE)

Arguments

cdsstr	StringVector [mandatory]
sgc	standard genetic code to use [default: 1]
method	KaKs Calculator 2.0 codon model [default: YN]
verbose	specify if verbose output [default: FALSE]

Value

list

Author(s)

Kristian K Ullrich

References

Wang et al. (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.Genomics, proteomics & bioinformatics. 8(1), 77-80.

Examples

## load example sequence data
data("hiv", package="MSA2dist")
rcpp_KaKs(cdsstr=as.character(hiv[1:3]))

kullrich/MSA2dist documentation built on April 26, 2024, 4:43 p.m.